TextureAtlas flips normals on half of the deep linked duplicates
So what fixed it for me was:


Select all objects and duplicate them by pressing Shift + D.
Make everything a single user object (hit U » Object &amp; Data).
Apply the scale and rotation with Ctrl+ A » Scale &amp; Rotation.
Go through each object with wrong normals and fix them (Tab to enter edit mode, select all by pressing A and then Ctrl + N to fix the normals)


When I then selected the Texture Atlas group and started the unwrapping everthing was fine, no flipped normals anymore.